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Werner appeared to be fouled by Ricardo Pereira in the first half, the striker having already seen a goal ruled out for offside and again later for handball.
"It's a clear penalty," Tuchel told Sky Sports. "These VAR decisions, honestly, they are horrible against us. It's the third time in a row.
"We had a goal against Arsenal, we had a goal against Leicester. This has to stop of course but we were not worried at half-time."
Tuchel was asked about Werner's performance, the reporter noting that the striker was "involved in everything."
"It's his job to be involved in everything and he needs to be involved on Sunday again," Tuchel replied. "It's not time now for extra praise. Enjoy, shut up, enjoy your free day and get ready for Sunday."
The Blues enacted revenge on Leicester after Saturday's FA Cup Final loss, winning 2-1 at Stamford Bridge to all but confirm their top-four place and throwing the Foxes' into doubt.
Tuchel says his Chelsea players will not be celebrating anything until after the Champions League Final.
He told BBC Sport: "It was a strong performance and well-deserved performance.
"No time for celebration, the job is not done yet, two more games to go. Very happy to play in front of supporters, it was a huge difference today."